Rings

Understanding Rings in SMILES

In SMILES, rings are represented by numbers that show where the ring opens and closes.

• The same number indicates start and end of a ring.

• Example:
  C1CCCCC1 → forms a 6-membered carbon ring (cyclohexane).
  The “1” after the first C means “start of ring 1,”
  and the “1” after the last C means “end of ring 1.

Let’s show this step-by-step in RDKit with simple examples.

1. Cyclopropane (Figure 1)

Code:

cyclopropane = Chem.MolFromSmiles("C1CC1")

cyclopropane

2. Cyclobutane (Figure 2)

Code:

cyclobutane = Chem.MolFromSmiles("C1CCC1")

cyclobutane

3. Cyclopentane (Figure 3)

Code:

cyclopentane = Chem.MolFromSmiles("C1CCCC1")

cyclopentane

4. Cyclohexene (Figure 4), A 6-membered ring with a double bond. 

The “=” indicates a double bond between C2 and C3. 

Code:

cyclohexene = Chem.MolFromSmiles("C1C=CCCC1")

cyclohexene

5. Cyclohexanol (Figure 5). The O in parentheses means the OH group branches off one of the carbons in the ring.  

Code:

cyclohexanol = Chem.MolFromSmiles("C1CC(O)CCC1")

cyclohexanol

6. Benzene (Figure 6). Lowercase “c” indicates aromatic carbon atoms

Code:

Benzene = Chem.MolFromSmiles("c1ccccc1")

Benzene

7. Naphthalene  (Figure 7). Two fused benzene rings. The numbers 1 and 2 below mark two ring closures, showing how rings can share atoms. 

Code:

naphthalene = Chem.MolFromSmiles("c1ccc2ccccc2c1")

naphthalene

8. Pyridine  (Figure 8). A six-membered aromatic ring with one nitrogen. 

Code:

pyridine = Chem.MolFromSmiles("c1ccncc1")

pyridine